How Do I Combine Transcipts To Quantify The Activity Of A Gene In A Microarray Experiment?
I have values on a log scale, from a microarray experiment. I want to measure the level of activity of various genes. If multiple transcripts map to the same gene, how do I combine the readings from different transcripts to quantify the activity of that gene?
Also, can anybody suggest a link to a good workflow on how to process microarray data, for instance how to do normalization?
My intent is to combine this microarray data with ChIP-seq data. Hopefully, I can say something about the level of activity of a gene and how it relates to my factor of interest.
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Depends strongly on which microarray platform the data come from?
It's affymetrix. Is that enough information or do I need to be more specific?
More specific - the exact platform. For example, summarizing exon arrays to gene level is very different to 3' arrays.